# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 00:33:14 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-nitrophenyl 6-thio-6-S-alpha-D-xylopyranosyl-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@H](SC[C@H]2O[C@@H](Oc3ccc(cc3)[N+]([O-])=O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H]1O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 XTG  XTG  '4-nitrophenyl 6-thio-6-S-alpha-D-xylopyranosyl-beta-D-glucopyranoside'  ligand  53  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XTG
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 XTG  C14   C  CR16   0  -0.340  -3.4448   2.9584  -0.7976
 XTG  C13   C  CR16   0  -0.254  -2.9732   4.2273  -0.5431
 XTG  C12   C  CR6    0   0.234  -1.8129   4.3825   0.2077
 XTG  N1    N  N      1   0.328  -1.3146   5.7120   0.4820
 XTG  O10   O  O     -1  -0.386  -1.9408   6.6555   0.0550
 XTG  O11   O  O      0  -0.386  -0.2954   5.8205   1.1254
 XTG  C17   C  CR16   0  -0.256  -1.1254   3.2802   0.6932
 XTG  C16   C  CR16   0  -0.343  -1.5951   2.0061   0.4331
 XTG  C15   C  CR6    0   0.405  -2.7654   1.8409  -0.3082
 XTG  O1    O  O2     0  -0.485  -3.3166   0.6506  -0.6077
 XTG  C1    C  CH1    0   0.258  -2.8699  -0.5092   0.0268
 XTG  O5    O  O2     0  -0.495  -1.6700  -0.8905  -0.5758
 XTG  C2    C  CH1    0  -0.024  -3.9276  -1.5904  -0.1751
 XTG  O2    O  OH1    0  -0.663  -5.1223  -1.2777   0.4903
 XTG  C3    C  CH1    0  -0.014  -3.3970  -2.8975   0.4061
 XTG  O3    O  OH1    0  -0.669  -4.2431  -3.9812   0.1156
 XTG  C4    C  CH1    0   0.050  -2.0199  -3.2263  -0.1659
 XTG  O4    O  OH1    0  -0.670  -1.4387  -4.3298   0.4768
 XTG  C5    C  CH1    0   0.022  -1.0926  -2.0292   0.0370
 XTG  C6    C  CH2    0  -0.576   0.2746  -2.2236  -0.5809
 XTG  S6    S  S2     0   0.011   1.2360  -0.6889  -0.3958
 XTG  C7    C  CH1    0  -0.119   2.8766  -1.3728  -0.0930
 XTG  O9    O  O2     0  -0.472   3.3852  -1.8642  -1.3054
 XTG  C11   C  CH2    0  -0.217   4.6479  -2.4775  -1.1383
 XTG  C10   C  CH1    0  -0.011   5.6917  -1.4830  -0.6539
 XTG  O8    O  OH1    0  -0.664   5.9615  -0.4800  -1.6019
 XTG  C9    C  CH1    0  -0.005   5.2028  -0.8007   0.6296
 XTG  O7    O  OH1    0  -0.670   5.1798  -1.7273   1.6920
 XTG  C8    C  CH1    0   0.012   3.7662  -0.2789   0.5023
 XTG  O6    O  OH1    0  -0.663   3.7516   0.8815  -0.2928
 XTG  H14   H  HCR6   0   0.288  -4.3491   2.8228  -1.3757
 XTG  H13   H  HCR6   0   0.300  -3.5137   5.0810  -0.9245
 XTG  H17   H  HCR6   0   0.301  -0.2195   3.3967   1.2701
 XTG  H16   H  HCR6   0   0.296  -1.0232   1.1658   0.7991
 XTG  H1    H  HCH1   0   0.227  -2.7243  -0.3242   1.1047
 XTG  H2    H  HCH1   0   0.237  -4.0841  -1.7175  -1.2561
 XTG  HO2   H  HOH1   0   0.461  -5.6100  -0.6301  -0.0277
 XTG  H3    H  HCH1   0   0.223  -3.2868  -2.7665   1.4944
 XTG  HO3   H  HOH1   0   0.459  -5.0505  -3.8909   0.6313
 XTG  H4    H  HCH1   0   0.220  -2.1233  -3.4025  -1.2482
 XTG  HO4   H  HOH1   0   0.457  -2.0152  -5.0914   0.3544
 XTG  H5    H  HCH1   0   0.241  -0.9687  -1.8506   1.1166
 XTG  H61   H  HCH2   0   0.275   0.1894  -2.4885  -1.6359
 XTG  H62   H  HCH2   0   0.288   0.7949  -3.0309  -0.0672
 XTG  H7    H  HCH1   0   0.255   2.7775  -2.1847   0.6417
 XTG  H111  H  HCH2   0   0.251   4.9305  -2.8916  -2.1090
 XTG  H112  H  HCH2   0   0.211   4.5878  -3.3163  -0.4325
 XTG  H10   H  HCH1   0   0.223   6.6051  -2.0491  -0.4111
 XTG  HO8   H  HOH1   0   0.452   6.3554  -0.8948  -2.3755
 XTG  H9    H  HCH1   0   0.236   5.8606   0.0498   0.8561
 XTG  HO7   H  HOH1   0   0.456   6.0599  -2.1035   1.7925
 XTG  H8    H  HCH1   0   0.249   3.4034  -0.0683   1.5156
 XTG  HO6   H  HOH1   0   0.458   3.1405   1.5112   0.0980

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 XTG  C14  C13   aromatic  1.377  0.020  1.377
 XTG  C14  C15   aromatic  1.396  0.020  1.396
 XTG  C14  H14   single    0.930  0.020  1.080
 XTG  C13  C12   aromatic  1.391  0.020  1.391
 XTG  C13  H13   single    0.930  0.020  1.080
 XTG  C12  N1    single    1.446  0.020  1.446
 XTG  C12  C17   aromatic  1.387  0.020  1.387
 XTG  N1   O10   single    1.210  0.020  1.210
 XTG  N1   O11   double    1.210  0.020  1.210
 XTG  C17  C16   aromatic  1.383  0.020  1.383
 XTG  C17  H17   single    0.930  0.020  1.080
 XTG  C16  C15   aromatic  1.395  0.020  1.395
 XTG  C16  H16   single    0.930  0.020  1.080
 XTG  C15  O1    single    1.346  0.020  1.346
 XTG  O1   C1    single    1.395  0.020  1.395
 XTG  C1   O5    single    1.396  0.020  1.396
 XTG  C1   C2    single    1.526  0.020  1.526
 XTG  C1   H1    single    0.970  0.020  1.090
 XTG  O5   C5    single    1.416  0.020  1.416
 XTG  C2   O2    single    1.403  0.020  1.403
 XTG  C2   C3    single    1.526  0.020  1.526
 XTG  C2   H2    single    0.970  0.020  1.090
 XTG  O2   HO2   single    0.850  0.020  0.980
 XTG  C3   O3    single    1.405  0.020  1.405
 XTG  C3   C4    single    1.527  0.020  1.527
 XTG  C3   H3    single    0.970  0.020  1.090
 XTG  O3   HO3   single    0.850  0.020  0.980
 XTG  C4   O4    single    1.403  0.020  1.403
 XTG  C4   C5    single    1.528  0.020  1.528
 XTG  C4   H4    single    0.970  0.020  1.090
 XTG  O4   HO4   single    0.850  0.020  0.980
 XTG  C5   C6    single    1.513  0.020  1.513
 XTG  C5   H5    single    0.970  0.020  1.090
 XTG  C6   S6    single    1.820  0.020  1.820
 XTG  C6   H61   single    0.970  0.020  1.090
 XTG  C6   H62   single    0.970  0.020  1.090
 XTG  S6   C7    single    1.803  0.020  1.803
 XTG  C7   O9    single    1.404  0.020  1.404
 XTG  C7   C8    single    1.530  0.020  1.530
 XTG  C7   H7    single    0.970  0.020  1.090
 XTG  O9   C11   single    1.414  0.020  1.414
 XTG  C11  C10   single    1.521  0.020  1.521
 XTG  C11  H111  single    0.970  0.020  1.090
 XTG  C11  H112  single    0.970  0.020  1.090
 XTG  C10  O8    single    1.406  0.020  1.406
 XTG  C10  C9    single    1.534  0.020  1.534
 XTG  C10  H10   single    0.970  0.020  1.090
 XTG  O8   HO8   single    0.850  0.020  0.980
 XTG  C9   O7    single    1.410  0.020  1.410
 XTG  C9   C8    single    1.534  0.020  1.534
 XTG  C9   H9    single    0.970  0.020  1.090
 XTG  O7   HO7   single    0.850  0.020  0.980
 XTG  C8   O6    single    1.407  0.020  1.407
 XTG  C8   H8    single    0.970  0.020  1.090
 XTG  O6   HO6   single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 XTG  H14   C14  C15   119.58  3.000
 XTG  H14   C14  C13   120.03  3.000
 XTG  C15   C14  C13   120.39  3.000
 XTG  H13   C13  C12   121.32  3.000
 XTG  H13   C13  C14   119.45  3.000
 XTG  C12   C13  C14   119.23  3.000
 XTG  C17   C12  N1    119.57  3.000
 XTG  C17   C12  C13   120.92  3.000
 XTG  N1    C12  C13   119.51  3.000
 XTG  O11   N1   O10   123.60  3.000
 XTG  O11   N1   C12   118.26  3.000
 XTG  O10   N1   C12   118.13  3.000
 XTG  H17   C17  C16   119.00  3.000
 XTG  H17   C17  C12   121.12  3.000
 XTG  C16   C17  C12   119.88  3.000
 XTG  H16   C16  C15   122.14  3.000
 XTG  H16   C16  C17   118.24  3.000
 XTG  C15   C16  C17   119.61  3.000
 XTG  O1    C15  C16   124.52  3.000
 XTG  O1    C15  C14   115.51  3.000
 XTG  C16   C15  C14   119.97  3.000
 XTG  C1    O1   C15   120.19  3.000
 XTG  H1    C1   C2    109.84  3.000
 XTG  H1    C1   O5    110.74  3.000
 XTG  C2    C1   O5    110.20  3.000
 XTG  H1    C1   O1    110.31  3.000
 XTG  C2    C1   O1    107.87  3.000
 XTG  O5    C1   O1    107.82  3.000
 XTG  C5    O5   C1    112.54  3.000
 XTG  H2    C2   C3    108.96  3.000
 XTG  H2    C2   O2    111.77  3.000
 XTG  C3    C2   O2    107.85  3.000
 XTG  H2    C2   C1    108.09  3.000
 XTG  C3    C2   C1    108.40  3.000
 XTG  O2    C2   C1    111.69  3.000
 XTG  HO2   O2   C2    109.05  3.000
 XTG  H3    C3   C4    107.78  3.000
 XTG  H3    C3   O3    110.86  3.000
 XTG  C4    C3   O3    107.43  3.000
 XTG  H3    C3   C2    108.01  3.000
 XTG  C4    C3   C2    110.82  3.000
 XTG  O3    C3   C2    111.87  3.000
 XTG  HO3   O3   C3    108.78  3.000
 XTG  H4    C4   C5    108.23  3.000
 XTG  H4    C4   O4    111.29  3.000
 XTG  C5    C4   O4    107.70  3.000
 XTG  H4    C4   C3    108.54  3.000
 XTG  C5    C4   C3    109.20  3.000
 XTG  O4    C4   C3    111.80  3.000
 XTG  HO4   O4   C4    108.41  3.000
 XTG  H5    C5   C6    108.64  3.000
 XTG  H5    C5   C4    109.00  3.000
 XTG  C6    C5   C4    113.18  3.000
 XTG  H5    C5   O5    109.86  3.000
 XTG  C6    C5   O5    107.16  3.000
 XTG  C4    C5   O5    108.97  3.000
 XTG  H62   C6   H61   108.26  3.000
 XTG  H62   C6   S6    108.94  3.000
 XTG  H61   C6   S6    110.13  3.000
 XTG  H62   C6   C5    109.53  3.000
 XTG  H61   C6   C5    110.83  3.000
 XTG  S6    C6   C5    109.11  3.000
 XTG  C7    S6   C6    100.25  3.000
 XTG  H7    C7   C8    108.68  3.000
 XTG  H7    C7   O9    110.57  3.000
 XTG  C8    C7   O9    112.07  3.000
 XTG  H7    C7   S6    108.08  3.000
 XTG  C8    C7   S6    108.85  3.000
 XTG  O9    C7   S6    108.51  3.000
 XTG  C11   O9   C7    111.93  3.000
 XTG  H112  C11  H111  107.20  3.000
 XTG  H112  C11  C10   109.42  3.000
 XTG  H111  C11  C10   110.69  3.000
 XTG  H112  C11  O9    111.00  3.000
 XTG  H111  C11  O9    106.88  3.000
 XTG  C10   C11  O9    111.53  3.000
 XTG  H10   C10  C9    107.96  3.000
 XTG  H10   C10  O8    110.86  3.000
 XTG  C9    C10  O8    107.94  3.000
 XTG  H10   C10  C11   107.65  3.000
 XTG  C9    C10  C11   109.79  3.000
 XTG  O8    C10  C11   112.54  3.000
 XTG  HO8   O8   C10   108.24  3.000
 XTG  H9    C9   C8    108.33  3.000
 XTG  H9    C9   O7    111.29  3.000
 XTG  C8    C9   O7    105.71  3.000
 XTG  H9    C9   C10   109.03  3.000
 XTG  C8    C9   C10   112.37  3.000
 XTG  O7    C9   C10   110.09  3.000
 XTG  HO7   O7   C9    108.70  3.000
 XTG  H8    C8   O6    111.12  3.000
 XTG  H8    C8   C9    107.37  3.000
 XTG  O6    C8   C9    109.71  3.000
 XTG  H8    C8   C7    107.72  3.000
 XTG  O6    C8   C7    111.33  3.000
 XTG  C9    C8   C7    109.49  3.000
 XTG  HO6   O6   C8    108.51  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 XTG  CONST_01  C17  C12  C13  C14    0.00   0.0  0
 XTG  CONST_02  C17  C16  C15  C14    0.00   0.0  0
 XTG  CONST_03  C16  C15  C14  C13    0.00   0.0  0
 XTG  CONST_04  C16  C17  C12  C13    0.00   0.0  0
 XTG  CONST_05  C15  C14  C13  C12    0.00   0.0  0
 XTG  CONST_06  C15  C16  C17  C12    0.00   0.0  0
 XTG  CONST_07  N1   C12  C13  C14  180.00   0.0  0
 XTG  CONST_08  O1   C15  C14  C13  180.00   0.0  0
 XTG  CONST_09  C16  C17  C12  N1   180.00   0.0  0
 XTG  CONST_10  O1   C15  C16  C17  180.00   0.0  0
 XTG  CONST_11  H16  C16  C15  C14  180.00   0.0  0
 XTG  CONST_12  H17  C17  C12  C13  180.00   0.0  0
 XTG  CONST_13  H14  C14  C13  C12  180.00   0.0  0
 XTG  CONST_14  H13  C13  C12  C17  180.00   0.0  0
 XTG  CONST_15  O10  N1   C12  C13    0.00   0.0  0
 XTG  CONST_16  O11  N1   C12  C13  180.00   0.0  0
 XTG  CONST_17  C17  C12  N1   O10  180.00   0.0  0
 XTG  CONST_18  C17  C12  N1   O11    0.00   0.0  0
 XTG  Var_01    C10  C11  O9   C7   -62.95  30.0  1
 XTG  Var_02    H61  C6   S6   C7   -94.97  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 XTG  chir_01  C1   O1  O5  C2   positiv
 XTG  chir_02  C2   O2  C1  C3   negativ
 XTG  chir_03  C3   O3  C2  C4   positiv
 XTG  chir_04  C4   O4  C3  C5   negativ
 XTG  chir_05  C5   O5  C4  C6   negativ
 XTG  chir_06  C7   S6  O9  C8   negativ
 XTG  chir_07  C10  O8  C9  C11  negativ
 XTG  chir_08  C9   O7  C8  C10  positiv
 XTG  chir_09  C8   O6  C9  C7   positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 XTG  plan-1  C14  0.020
 XTG  plan-1  C13  0.020
 XTG  plan-1  C12  0.020
 XTG  plan-1  N1   0.020
 XTG  plan-1  C17  0.020
 XTG  plan-1  C16  0.020
 XTG  plan-1  C15  0.020
 XTG  plan-1  O1   0.020
 XTG  plan-1  H14  0.020
 XTG  plan-1  H13  0.020
 XTG  plan-1  H17  0.020
 XTG  plan-1  H16  0.020
 XTG  plan-2  C12  0.020
 XTG  plan-2  N1   0.020
 XTG  plan-2  O10  0.020
 XTG  plan-2  O11  0.020

